how to import a 1000 genome project vcf file (chromosome file) into a mysql database
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6.1 years ago
pinikoma • 0

Hi All

I would like to  import / upload a 1000 genome project vcf file (chromosome file) into a mysql database using sql.

if there are existing mysql dumps , please tell where I can find them ,

also if there is an official way-script I would love to see it

 

thanks, pini.

 

1000 genome project vcf mysql schema chromosome • 2.5k views
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see Do People Import Vcf Files Into Databases? , Vcf Database Table Structure  . But inserting a VCF into a database is a bad idea unless you want to expose your data. Tabix/Tribble indexes  should do the job.

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Meanwhile, Ensembl has stopped putting a lot of variation data into MySQL and instead are storing everything in VCFs (much more compact).

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How would you import anything to a database? See programming forums for a batch insert command.
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